Ab initio QM/MM study shows there is no general acid in the reaction catalyzed by 4-oxalocrotonate tautomerase

Journal of the American Chemical Society

Volumn 125, Issue 34, 2003, Pages 10384-10393

  Cisneros, G Andrés ^a   Liu, Haiyan ^a,b   Zhang, Yingkai ^a,c   Yang, Weitao ^a  

^a DUKE UNIVERSITY   (United States)

^b UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

^c HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYSTS; ENZYMES; FREE ENERGY; HYDROGEN BONDS; QUANTUM THEORY;

MOLECULAR MECHANICAL (MM) METHODS;

REACTION KINETICS;

4 OXALOCROTONATE TAUTOMERASE; ARGININE; CARBON; CARBOXYLIC ACID; CROTONIC ACID DERIVATIVE; PROTON; UNCLASSIFIED DRUG;

AB INITIO CALCULATION; AMINO TERMINAL SEQUENCE; ARTICLE; CATALYSIS; CHEMICAL REACTION; HYDROGEN BOND; MOLECULAR MECHANICS; QUANTUM MECHANICS; REACTION ANALYSIS;

EID: 0042431983     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja029672a     Document Type: Article

References (31)

1. Chen, L. H.; Kenyon, G. L.; Curtin, F.; Harayama, S.; Bembenek, M. E.; Hajipour, G.; Whitman, C. P. J. Biol. Chem. 1992, 267, 17716.
2. Harayama, S.; M. Rekik, K.-L. N.; Ornston, L. J. Bacteriol. 1989, 171, 6251.
3. Stivers, J. T.; Abeygunawardana, C.; Whitman, C. P.; Mildvan, A. S. Protein Sci. 1996, 5, 729.
4. Taylor, A. B.; Czerwinski, R. M.; Johnson, W. H., Jr.; Whitman, C. P.; Hackert, M. L. Biochemistry 1998, 37, 14692.
5. Lian, H.; Whitman, C. P. J. Am. Chem. Soc. 1993, 115, 7978.
6. Stivers, J. T.; Abeygunawardana, C.; Mildvan, A. S.; Hajipour, G.; Whitman, C. P.; Chen, L. H. Biochemistry 1996, 35, 803.
7. Fitzgerald, M. C.; Chernushevich, I.; Standing, K. G.; Whitman, C. P.; Kent, S. B. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 6851.
8. Czerwinski, R. M.; Johnson, W. H., Jr.; Whitman, C. P.; Harris, T. K.; Abeygunawardana, C.; Mildvan, A. S. Biochemistry 1997, 36, 14551.
9. Harris, T. K.; Czerwinski, R. M.; Johnson, W. H., Jr.; Legler, P. M.; Abeygunawardana, C.; Massiah, M. A.; Stivers, J. T.; Whitman, C. P.; Mildvan, A. S. Biochemistry 1999, 38, 12343.
10. Whitman, C. Arch. Biochem. Biophys. 2002, 402, 1.
11. Soares, T.; Goddsell, D.; Briggs, J.; Ferreira, R.; Olson, A. Biopolymers 1999, 50, 319.
12. Czerwinski, R. M.; Harris, T. K.; Johnson, W. H., Jr.; Legler, P. M.; Stivers, J. T.; Mildvan, A. S.; Whitman, C. P. Biochemistry 1999, 38, 12358.
13. Warshel, A.; Levitt, M. J. Mol. Biol. 1976, 103, 227.
14. Zhang, Y.; Lee, T.; Yang, W. J. Chem. Phys. 1999, 110, 46.
15. Zhang, Y.; Liu, H.; Yang, W. J. Chem. Phys. 2000, 112, 3483.
16. Zhang, Y.; Liu, H.; Yang, W. Ab Initio QM/MM and Free Energy Calculations of Enzyme Reactions. In Computational Methods for Macromolecules-Challenges and Applications; Springer-Verlag: Heidelberg, Germany, 2002.
17. Frisch, M. J.; et al. Gaussian 98, revision A.8; Gaussian. Inc.: Pittsburgh, PA, 1998.
18. Ponder, J. TINKER, Software Tools for Molecular Design, Version 3.6: the most updated version for the TINKER program can be obtained from J. W. Ponder's WWW site at http://dasher.wustl.edu/tinker.; Washington University: St. Louis, MO. 1998.
19. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179.
20. Jorgensen, W.; Chandrasekhar, J.; Madura, J.; Impey, R.; Klein, M. J. Chem. Phys. 1983, 79, 926.
21. Besler, B.; Merz, K. M., Jr.; Kollman, P. J. Comput. Chem. 1990, 11, 431.
22. Williams, I.; Maggiora, G. J. Mol. Struct. 1982, 89, 365.
23. Foresman, J.; Frisch, A. Exploring Chemistry with Electronic Structure Methods; Gaussian Inc.: Pittsburgh, PA, 1996.
24. Zwanzig, R. W. J. Chem. Phys. 1954, 22, 1420-1426.
25. Johnson, W. H.; Czerwinski, R. M.; Fitzgerald, M. C.; Whitman, C. P. Biochemistry 1997, 36, 15724.
26. Whitman, C. P.; Aird, B.; Gillespie, W.; Stolowich, N. J. Am. Chem. Soc. 1991, 113, 3154.
27. van Gunsteren, W.; Berendsen, H.; Colonna, F.; Perahia, D.; Hollenberg, J.; Lellouch, D. J. Comput. Chem. 1984, 5, 272.
28. Ryckaert, J.; Ciccotti, G.; Berendsen, H. J. Comput. Phys. 1977, 23, 327.
29. Stivers, J. T.; Abeygunawardana, C.; Mildvan, A. S.; Hajipour, G.; Whitman, C. P. Biochemistry 1996, 35, 814.
30. Liu, H.; Zhang, Y.; Yang, W. J. Am. Chem. Soc. 2000, 122, 6560.
31. Czerwinski, R. M.; Harris, T. K.; Massiah, M. A.; Mildvan, A. S.; Whitman, C. P. Biochemistry 2001, 40, 1984.